HerbertMistry 1

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DNA Oxidation Basics of Repair
Virtual Free Radical School
Karl E. Herbert, Ph.D. Pratibha Mistry,
Ph.D. Faculty of Medicine Biological Sciences,
University of Leicester, Leicester, UK
feedback keh3_at_le.ac.uk
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Overview

• DNA damage
• base excision repair (BER)
• global genome (GG) transcription coupled (TC)
  nucleotide excision repair (NER)
• sanitization of the deoxynucleotide pool

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Consequences of DNA damage
DNA DAMAGE
DNA REPAIR MECHANISMS
SHORT-TERM CONSEQUENCES
ABNORMAL GROWTH METABOLISM
PHYSIOLOGICAL DYSFUNCTION
CELL DEATH
Decreased cellular proliferation
Defective signalling pathways
Impaired protein/ gene expression
Genomic instability
LONG-TERM CONSEQUENCES
Ageing
Cancer
Disease
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Types of oxidative DNA damage

• purine pyrimidine oxidation products
• abasic (AP) sites
• strand breaks

• see Schafer, SFRBM Education Program
  presentation
• http//www.medicine.uiowa.edu/frrb/
  VirtualSchool/Virtual.html

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BER

• non-bulky lesions, abasic sites strand breaks
  are repaired by BER
• mono- or bifunctional lesion-specific
  glycosylases may initiate repair by the
  cleavage of the N-C1 glycosidic bond between
  the base deoxyribose- phosphate backbone
  leaving an abasic site
• following the removal of abasic sites, short or
  long-patch BER resumes resulting in the repair
  of a single or 2-8 nucleotide gap, respectively

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BER enzymes e.g. functional diversity I
MutM/fpg formamidopyrimidine glycosylase endo
VIII/Nei endonuclease VIII OGG 8-oxoguanine
DNA glycosylase NEIL Nei endonuclease
VIII-like MPG N-methylpurine-DNA glycosylase
AlkA 3-methyladenine DNA glycosylase II
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BER enzymes e.g. functional diversity II
endo III endonucleases III Ntg endonuclease
III-like glycosylase NTHL1 Nth endonuclease
III-like 1 TDG thymine-DNA glycosylase
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Short-patch BER
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BER of 8-oxoG
hAPE/HAP1/REF1 apurinic/apyrimidinic endonuclease
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Other BER Proteins
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Long-patch BER
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DNA repair pathways the prevention of mutations
Complexities of DNA repair pathways replication
..specific enzymes prevent incorrect base pairing
opposite DNA lesions during DNA replication
Sanitization of the deoxynucleotide pool...
..specific enzymes prevent the incorporation of
damaged deoxynucleotides opposite a template
strand during DNA replication
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Complexities of repair pathways replication..
template strand
misincorporation
oxidation
A/T/G
?
?
G
C
good ?
bad X
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Sanitization of the deoxynucleotide pool..
prevents incorporation of 8-oxoG into DNA
MutT nucleoside triphosphate pyrophosphohydrolase
NUDT1 nudix (nucleoside diphosphate linked
moiety X)- type motif 1 hMTH1 human homolog of
MutT
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GG TC NER

• bulky small lesions causing differing degrees
  of DNA distortion are removed by NER
• NER is implicated as a back-up system for BER
• different complexes initiate NER in transcribed
  non-transcribed DNA
• NER involves the dual incision of unwound DNA
  either side of the lesion by a multisubunit
  ATP-dependent nuclease the release of a 24-29
  oligomer
• the resultant gap is filled sealed by the
  action of various components including DNA
  polymerases ligases

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GG TC NER
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Bibliography
Human DNA Repair Enzymes http//www.cgal.icnet.u
k/DNA_Repair_Genes.html Boiteux S and Radicella
JP (2000). The human OGG1 gene structure,
functions and its implication in the process of
carcinogenesis. Arch Biochem Biophys. 377
1-8 Friedberg EC (1996). Relationships between
DNA repair and transcription. Ann Rev Biochem.
65 15-42 Hanawalt PC (1995). DNA repair comes
of age. Mutat Res. 336 101-113 Hazra TK,
Izumi T, Boldogh I, Imhoff B, Kow YW, Jaruga P,
Dizdaroglu M and Mitra S (2002). Identification
and characterization of a human DNA glycosylase
for repair of modified bases in oxidatively
damaged DNA. Proc Natl Acad Sci USA 99
3523-3528 Hoeijmakers JHJ (2001). Genome
maintenance mechanisms for preventing cancer.
Nature. 411 366-374 Krokan HE, Nilsen H,
Skorpen F, Otterlei M and Slupphaug G (2000).
Base excision repair of DNA in mammalian cells.
FEBS Lett. 476 73-77 Lindahl T and Wood RD
(1999). Quality control by DNA repair.
Science. 286 1897-1905 Mitra S (1999). Repair
of oxidative DNA damage and aging central role
of AP-endonuclease. In Dizdaroglu and Karakaya,
eds. Advances in DNA Damage and Repair, Kluwer
Academic, Plenum Publishers, New York. pp
295-311 Sancar A (1996). DNA excision repair.
Ann Rev Biochem. 65 43-81